Configuration of Motif Logos

When RGT is installed, it will automatically create a folder to store additional data (default: ~/rgtdata). This data regards chromosome sizes, position frequency matrices (describing transcription factor motifs), HTML scripts, etc. Some tools require data which is too big to fit in the installation procedure such as motif logos. In this section we will describe how to obtain the motif logo graphs (graphical representation of position weight matrices (PWMs)).

The following command will generate motif logos for the main repositories being used (JASPAR vertebrates and UNIPROBE primary motifs):

cd ~/rgtdata
python setupLogoData.py --jaspar-vertebrates --uniprobe-primary

The following command will generate motif logos for all the PWMs inside the motifs’ repositories data path. The logos data path is structured the same way as the motifs data path (data from each repository in a separate folder).

cd ~/rgtdata
python setupLogoData.py --all

This script has further options that can be viewed with

python setupLogoData.py -h